[gmx-users] position of water molecules during the simulation time

Justin Lemkul jalemkul at vt.edu
Wed May 3 14:09:08 CEST 2017

On 5/3/17 2:33 AM, Nikhil Maroli wrote:
> Dear all,
> I wanted to calculate the position of the water molecules during the
> simulation time. This is for understanding the movements of water molecules
> through a channel protein. How I can get this information using gromacs.
> I'm looking for something like this in Fig (b)
> https://drive.google.com/file/d/0BxaQk_pcR9viS3I3NDlKSURuUGs/view?usp=sharing

This can be done with gmx traj -ox -z.  Choose which waters to monitor via gmx 
select or some other suitable criteria.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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